Sardine MSE Result Notes
Robert Wildermuth
7/26/2021
Evaluation of sardine cohort growth operating model
The following notes document the results of applying a 6 year projection to Peter Kuriyama’s cohort growth Stock Synthesis model for Pacific sardine using {SSMSE}. The separate runs progress from a self test to applying additional sampling error in the SSMSE sampling module.
Self test with only acoustic-trawl index specified
# read in SSMSE results summary
tsSumry <- read.csv("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/results_ts_cohortGrowthselftest.csv")
# Get rid of duplicated SSB years
tsSumry <- na.omit(tsSumry)
# bring in simulated data for each iteration to plot with OM and EM vals
simDat <- data.frame()
for(i in c(2,4:9)){
itDat <- SS_readdat(file = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/",
i, "/cohortGrowthOMandEM_EM_2024/data.ss_new"),
version = "3.30")[["CPUE"]] %>%
filter(index == 4) %>%
mutate(iteration = i,
model_run = "cohortGrowthselftest_data")
simDat <- rbind(simDat, itDat)
}## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999# simDat <- SS_readdat(file = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/data.ss_new",
# version = "3.30")[["CPUE"]] %>%
# filter(index == 4) %>%
# mutate(#iteration = i,
# model_run = "cohortGrowthselftest_data")
# plots of simulated and estimated biomass trends per iteration
ggplot2::ggplot(data = subset(tsSumry, model_run %in% c("0_estimate_cohort_growh_OM",
"cohortGrowthOMandEM_EM_2020",
"cohortGrowthOMandEM_EM_2021",
"cohortGrowthOMandEM_EM_2022",
"cohortGrowthOMandEM_EM_2023",
"cohortGrowthOMandEM_EM_2024")),
ggplot2::aes(x = year, y = SpawnBio)) +
ggplot2::geom_vline(xintercept = 2019, color = "gray") +
geom_point(data = simDat, mapping = aes(x = year, y = obs), shape = 4, color = "grey") +
ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = model_run))+
ggplot2::scale_color_manual(values = c("#D65F00", rep("black", 4), "blue")) +
ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
ggplot2::guides(linetype = FALSE) +
ggplot2::facet_wrap(. ~ iteration) +
ggplot2::theme_classic()## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
# plot of OM and EM and simulated data
indexPlot <- plot_index_sampling(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest")## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.# !!RW: sampled_dataset are different among iterations
indexPlot # !RW: only getting last three iterations, but gets the point across ## $index_dat
## year seas index obs se_log iteration scenario
## 1 2005 10 4 1947060.00 0.300 2 cohortGrowthselftest
## 2 2007 10 4 751075.00 0.090 2 cohortGrowthselftest
## 3 2009 10 4 357006.00 0.410 2 cohortGrowthselftest
## 4 2010 10 4 493672.00 0.300 2 cohortGrowthselftest
## 5 2011 10 4 469480.00 0.280 2 cohortGrowthselftest
## 6 2012 10 4 305146.00 0.240 2 cohortGrowthselftest
## 7 2013 10 4 35339.00 0.380 2 cohortGrowthselftest
## 8 2014 10 4 29048.00 0.290 2 cohortGrowthselftest
## 9 2015 10 4 83030.00 0.470 2 cohortGrowthselftest
## 10 2008 1 4 801000.00 0.300 2 cohortGrowthselftest
## 11 2012 1 4 340831.00 0.330 2 cohortGrowthselftest
## 12 2013 1 4 306191.00 0.293 2 cohortGrowthselftest
## 13 2014 1 4 26279.00 0.697 2 cohortGrowthselftest
## 14 2015 1 4 16375.00 0.940 2 cohortGrowthselftest
## 15 2016 1 4 72867.00 0.497 2 cohortGrowthselftest
## 16 2017 1 4 14103.00 0.300 2 cohortGrowthselftest
## 17 2018 1 4 25148.00 0.670 2 cohortGrowthselftest
## 18 2019 1 4 33632.00 0.190 2 cohortGrowthselftest
## 25 1986 1 5 4061.00 0.600 2 cohortGrowthselftest
## 26 1987 1 5 8661.00 0.560 2 cohortGrowthselftest
## 27 1993 10 5 69065.00 0.290 2 cohortGrowthselftest
## 28 2003 10 5 145274.00 0.230 2 cohortGrowthselftest
## 29 2004 10 5 459943.00 0.550 2 cohortGrowthselftest
## 30 2006 10 5 198404.00 0.300 2 cohortGrowthselftest
## 31 2007 10 5 66395.00 0.270 2 cohortGrowthselftest
## 32 2008 10 5 99162.00 0.240 2 cohortGrowthselftest
## 33 2009 10 5 58447.00 0.400 2 cohortGrowthselftest
## 34 2010 10 5 219386.00 0.270 2 cohortGrowthselftest
## 35 2011 10 5 113178.00 0.270 2 cohortGrowthselftest
## 36 2012 10 5 82182.00 0.290 2 cohortGrowthselftest
## 37 2014 10 5 19376.00 0.540 2 cohortGrowthselftest
## 38 1986 1 6 11220.00 0.730 2 cohortGrowthselftest
## 39 1987 1 6 25637.00 0.480 2 cohortGrowthselftest
## 40 1987 10 6 17266.00 0.350 2 cohortGrowthselftest
## 41 1993 10 6 73374.00 0.210 2 cohortGrowthselftest
## 42 1995 10 6 97923.00 0.400 2 cohortGrowthselftest
## 43 1996 10 6 482246.00 0.210 2 cohortGrowthselftest
## 44 1997 10 6 369775.00 0.330 2 cohortGrowthselftest
## 45 1998 10 6 332177.00 0.340 2 cohortGrowthselftest
## 46 1999 10 6 1252540.00 0.390 2 cohortGrowthselftest
## 47 2000 10 6 931377.00 0.380 2 cohortGrowthselftest
## 48 2001 10 6 236660.00 0.170 2 cohortGrowthselftest
## 49 2002 10 6 556177.00 0.180 2 cohortGrowthselftest
## 50 2003 10 6 307795.00 0.240 2 cohortGrowthselftest
## 51 2004 10 6 486950.00 0.400 2 cohortGrowthselftest
## 52 2005 10 6 651994.00 0.250 2 cohortGrowthselftest
## 53 2006 10 6 306297.00 0.260 2 cohortGrowthselftest
## 54 2007 10 6 128118.00 0.210 2 cohortGrowthselftest
## 55 2008 10 6 162188.00 0.220 2 cohortGrowthselftest
## 56 2009 10 6 97838.00 0.390 2 cohortGrowthselftest
## 57 2010 10 6 364798.00 0.260 2 cohortGrowthselftest
## 58 2011 10 6 227632.00 0.270 2 cohortGrowthselftest
## 59 2012 10 6 198472.00 0.290 2 cohortGrowthselftest
## 60 2014 10 6 30396.00 0.660 2 cohortGrowthselftest
## 61 2005 10 4 1101140.00 0.300 2 cohortGrowthselftest
## 62 2007 10 4 944250.00 0.090 2 cohortGrowthselftest
## 63 2009 10 4 485467.00 0.410 2 cohortGrowthselftest
## 64 2010 10 4 383976.00 0.300 2 cohortGrowthselftest
## 65 2011 10 4 370126.00 0.280 2 cohortGrowthselftest
## 66 2012 10 4 200798.00 0.240 2 cohortGrowthselftest
## 67 2013 10 4 84678.00 0.380 2 cohortGrowthselftest
## 68 2014 10 4 41015.20 0.290 2 cohortGrowthselftest
## 69 2015 10 4 40131.40 0.470 2 cohortGrowthselftest
## 70 2008 1 4 967167.00 0.300 2 cohortGrowthselftest
## 71 2012 1 4 348700.00 0.330 2 cohortGrowthselftest
## 72 2013 1 4 179274.00 0.293 2 cohortGrowthselftest
## 73 2014 1 4 76487.80 0.697 2 cohortGrowthselftest
## 74 2015 1 4 36195.70 0.940 2 cohortGrowthselftest
## 75 2016 1 4 43199.80 0.497 2 cohortGrowthselftest
## 76 2017 1 4 45528.50 0.300 2 cohortGrowthselftest
## 77 2018 1 4 41429.60 0.670 2 cohortGrowthselftest
## 78 2019 1 4 33218.90 0.190 2 cohortGrowthselftest
## 85 1986 1 5 4354.10 0.600 2 cohortGrowthselftest
## 86 1987 1 5 4891.42 0.560 2 cohortGrowthselftest
## 87 1993 10 5 26846.30 0.290 2 cohortGrowthselftest
## 88 2003 10 5 67235.50 0.230 2 cohortGrowthselftest
## 89 2004 10 5 80905.40 0.550 2 cohortGrowthselftest
## 90 2006 10 5 141476.00 0.300 2 cohortGrowthselftest
## 91 2007 10 5 133955.00 0.270 2 cohortGrowthselftest
## 92 2008 10 5 108731.00 0.240 2 cohortGrowthselftest
## 93 2009 10 5 76562.70 0.400 2 cohortGrowthselftest
## 94 2010 10 5 55439.30 0.270 2 cohortGrowthselftest
## 95 2011 10 5 55613.60 0.270 2 cohortGrowthselftest
## 96 2012 10 5 34929.00 0.290 2 cohortGrowthselftest
## 97 2014 10 5 7236.38 0.540 2 cohortGrowthselftest
## 98 1986 1 6 15046.10 0.730 2 cohortGrowthselftest
## 99 1987 1 6 16902.80 0.480 2 cohortGrowthselftest
## 100 1987 10 6 29702.40 0.350 2 cohortGrowthselftest
## 101 1993 10 6 92770.30 0.210 2 cohortGrowthselftest
## 102 1995 10 6 307084.00 0.400 2 cohortGrowthselftest
## 103 1996 10 6 443438.00 0.210 2 cohortGrowthselftest
## 104 1997 10 6 479106.00 0.330 2 cohortGrowthselftest
## 105 1998 10 6 497986.00 0.340 2 cohortGrowthselftest
## 106 1999 10 6 578660.00 0.390 2 cohortGrowthselftest
## 107 2000 10 6 556682.00 0.380 2 cohortGrowthselftest
## 108 2001 10 6 427305.00 0.170 2 cohortGrowthselftest
## 109 2002 10 6 328371.00 0.180 2 cohortGrowthselftest
## 110 2003 10 6 232340.00 0.240 2 cohortGrowthselftest
## 111 2004 10 6 279578.00 0.400 2 cohortGrowthselftest
## 112 2005 10 6 416060.00 0.250 2 cohortGrowthselftest
## 113 2006 10 6 488886.00 0.260 2 cohortGrowthselftest
## 114 2007 10 6 462898.00 0.210 2 cohortGrowthselftest
## 115 2008 10 6 375733.00 0.220 2 cohortGrowthselftest
## 116 2009 10 6 264571.00 0.390 2 cohortGrowthselftest
## 117 2010 10 6 191577.00 0.260 2 cohortGrowthselftest
## 118 2011 10 6 192179.00 0.270 2 cohortGrowthselftest
## 119 2012 10 6 120701.00 0.290 2 cohortGrowthselftest
## 120 2014 10 6 25006.10 0.660 2 cohortGrowthselftest
## 121 2005 10 4 1849260.00 0.300 2 cohortGrowthselftest
## 122 2007 10 4 736232.00 0.090 2 cohortGrowthselftest
## 123 2009 10 4 352322.00 0.410 2 cohortGrowthselftest
## 124 2010 10 4 369430.00 0.300 2 cohortGrowthselftest
## 125 2011 10 4 718850.00 0.280 2 cohortGrowthselftest
## 126 2012 10 4 273730.00 0.240 2 cohortGrowthselftest
## 127 2013 10 4 72283.40 0.380 2 cohortGrowthselftest
## 128 2014 10 4 66719.80 0.290 2 cohortGrowthselftest
## 129 2015 10 4 54881.80 0.470 2 cohortGrowthselftest
## 130 2008 1 4 783588.00 0.300 2 cohortGrowthselftest
## 131 2012 1 4 267836.00 0.330 2 cohortGrowthselftest
## 132 2013 1 4 166505.00 0.293 2 cohortGrowthselftest
## 133 2014 1 4 87074.70 0.697 2 cohortGrowthselftest
## 134 2015 1 4 156470.00 0.940 2 cohortGrowthselftest
## 135 2016 1 4 40421.80 0.497 2 cohortGrowthselftest
## 136 2017 1 4 64717.40 0.300 2 cohortGrowthselftest
## 137 2018 1 4 72090.70 0.670 2 cohortGrowthselftest
## 138 2019 1 4 36175.30 0.190 2 cohortGrowthselftest
## 139 1986 1 5 4687.39 0.600 2 cohortGrowthselftest
## 140 1987 1 5 6368.65 0.560 2 cohortGrowthselftest
## 141 1993 10 5 47161.60 0.290 2 cohortGrowthselftest
## 142 2003 10 5 57147.20 0.230 2 cohortGrowthselftest
## 143 2004 10 5 241352.00 0.550 2 cohortGrowthselftest
## 144 2006 10 5 94080.10 0.300 2 cohortGrowthselftest
## 145 2007 10 5 165026.00 0.270 2 cohortGrowthselftest
## 146 2008 10 5 100034.00 0.240 2 cohortGrowthselftest
## 147 2009 10 5 62249.20 0.400 2 cohortGrowthselftest
## 148 2010 10 5 62577.90 0.270 2 cohortGrowthselftest
## 149 2011 10 5 47105.10 0.270 2 cohortGrowthselftest
## 150 2012 10 5 33411.70 0.290 2 cohortGrowthselftest
## 151 2014 10 5 21391.10 0.540 2 cohortGrowthselftest
## 152 1986 1 6 7264.25 0.730 2 cohortGrowthselftest
## 153 1987 1 6 25226.50 0.480 2 cohortGrowthselftest
## 154 1987 10 6 33161.60 0.350 2 cohortGrowthselftest
## 155 1993 10 6 126418.00 0.210 2 cohortGrowthselftest
## 156 1995 10 6 235376.00 0.400 2 cohortGrowthselftest
## 157 1996 10 6 371177.00 0.210 2 cohortGrowthselftest
## 158 1997 10 6 681632.00 0.330 2 cohortGrowthselftest
## 159 1998 10 6 773135.00 0.340 2 cohortGrowthselftest
## 160 1999 10 6 515309.00 0.390 2 cohortGrowthselftest
## 161 2000 10 6 688020.00 0.380 2 cohortGrowthselftest
## 162 2001 10 6 377793.00 0.170 2 cohortGrowthselftest
## 163 2002 10 6 324992.00 0.180 2 cohortGrowthselftest
## 164 2003 10 6 148135.00 0.240 2 cohortGrowthselftest
## 165 2004 10 6 670079.00 0.400 2 cohortGrowthselftest
## 166 2005 10 6 350421.00 0.250 2 cohortGrowthselftest
## 167 2006 10 6 630179.00 0.260 2 cohortGrowthselftest
## 168 2007 10 6 267310.00 0.210 2 cohortGrowthselftest
## 169 2008 10 6 378205.00 0.220 2 cohortGrowthselftest
## 170 2009 10 6 201204.00 0.390 2 cohortGrowthselftest
## 171 2010 10 6 208797.00 0.260 2 cohortGrowthselftest
## 172 2011 10 6 225686.00 0.270 2 cohortGrowthselftest
## 173 2012 10 6 87803.90 0.290 2 cohortGrowthselftest
## 174 2014 10 6 24344.90 0.660 2 cohortGrowthselftest
## 175 2005 10 4 1273580.00 0.300 4 cohortGrowthselftest
## 176 2007 10 4 956795.00 0.090 4 cohortGrowthselftest
## 177 2009 10 4 833354.00 0.410 4 cohortGrowthselftest
## 178 2010 10 4 329810.00 0.300 4 cohortGrowthselftest
## 179 2011 10 4 328997.00 0.280 4 cohortGrowthselftest
## 180 2012 10 4 188288.00 0.240 4 cohortGrowthselftest
## 181 2013 10 4 45838.30 0.380 4 cohortGrowthselftest
## 182 2014 10 4 47527.60 0.290 4 cohortGrowthselftest
## 183 2015 10 4 66378.60 0.470 4 cohortGrowthselftest
## 184 2008 1 4 1095470.00 0.300 4 cohortGrowthselftest
## 185 2012 1 4 319878.00 0.330 4 cohortGrowthselftest
## 186 2013 1 4 146493.00 0.293 4 cohortGrowthselftest
## 187 2014 1 4 80463.80 0.697 4 cohortGrowthselftest
## 188 2015 1 4 60785.50 0.940 4 cohortGrowthselftest
## 189 2016 1 4 83395.40 0.497 4 cohortGrowthselftest
## 190 2017 1 4 63344.30 0.300 4 cohortGrowthselftest
## 191 2018 1 4 27301.00 0.670 4 cohortGrowthselftest
## 192 2019 1 4 31728.10 0.190 4 cohortGrowthselftest
## 193 1986 1 5 1840.14 0.600 4 cohortGrowthselftest
## 194 1987 1 5 12034.40 0.560 4 cohortGrowthselftest
## 195 1993 10 5 24993.50 0.290 4 cohortGrowthselftest
## 196 2003 10 5 61183.10 0.230 4 cohortGrowthselftest
## 197 2004 10 5 85559.70 0.550 4 cohortGrowthselftest
## 198 2006 10 5 173592.00 0.300 4 cohortGrowthselftest
## 199 2007 10 5 107337.00 0.270 4 cohortGrowthselftest
## 200 2008 10 5 191128.00 0.240 4 cohortGrowthselftest
## 201 2009 10 5 107944.00 0.400 4 cohortGrowthselftest
## 202 2010 10 5 45362.60 0.270 4 cohortGrowthselftest
## 203 2011 10 5 80481.20 0.270 4 cohortGrowthselftest
## 204 2012 10 5 33414.40 0.290 4 cohortGrowthselftest
## 205 2014 10 5 19364.10 0.540 4 cohortGrowthselftest
## 206 1986 1 6 17133.10 0.730 4 cohortGrowthselftest
## 207 1987 1 6 12026.10 0.480 4 cohortGrowthselftest
## 208 1987 10 6 29926.30 0.350 4 cohortGrowthselftest
## 209 1993 10 6 89433.50 0.210 4 cohortGrowthselftest
## 210 1995 10 6 214749.00 0.400 4 cohortGrowthselftest
## 211 1996 10 6 416808.00 0.210 4 cohortGrowthselftest
## 212 1997 10 6 760750.00 0.330 4 cohortGrowthselftest
## 213 1998 10 6 513017.00 0.340 4 cohortGrowthselftest
## 214 1999 10 6 620087.00 0.390 4 cohortGrowthselftest
## 215 2000 10 6 1207500.00 0.380 4 cohortGrowthselftest
## 216 2001 10 6 638326.00 0.170 4 cohortGrowthselftest
## 217 2002 10 6 283222.00 0.180 4 cohortGrowthselftest
## 218 2003 10 6 223028.00 0.240 4 cohortGrowthselftest
## 219 2004 10 6 201695.00 0.400 4 cohortGrowthselftest
## 220 2005 10 6 594578.00 0.250 4 cohortGrowthselftest
## 221 2006 10 6 420836.00 0.260 4 cohortGrowthselftest
## 222 2007 10 6 448229.00 0.210 4 cohortGrowthselftest
## 223 2008 10 6 342041.00 0.220 4 cohortGrowthselftest
## 224 2009 10 6 292266.00 0.390 4 cohortGrowthselftest
## 225 2010 10 6 217327.00 0.260 4 cohortGrowthselftest
## 226 2011 10 6 186836.00 0.270 4 cohortGrowthselftest
## 227 2012 10 6 121746.00 0.290 4 cohortGrowthselftest
## 228 2014 10 6 91560.10 0.660 4 cohortGrowthselftest
## 229 2005 10 4 1236650.00 0.300 5 cohortGrowthselftest
## 230 2007 10 4 1052950.00 0.090 5 cohortGrowthselftest
## 231 2009 10 4 273910.00 0.410 5 cohortGrowthselftest
## 232 2010 10 4 397137.00 0.300 5 cohortGrowthselftest
## 233 2011 10 4 481964.00 0.280 5 cohortGrowthselftest
## 234 2012 10 4 228273.00 0.240 5 cohortGrowthselftest
## 235 2013 10 4 54517.10 0.380 5 cohortGrowthselftest
## 236 2014 10 4 81714.60 0.290 5 cohortGrowthselftest
## 237 2015 10 4 15419.10 0.470 5 cohortGrowthselftest
## 238 2008 1 4 908212.00 0.300 5 cohortGrowthselftest
## 239 2012 1 4 222648.00 0.330 5 cohortGrowthselftest
## 240 2013 1 4 152144.00 0.293 5 cohortGrowthselftest
## 241 2014 1 4 70841.50 0.697 5 cohortGrowthselftest
## 242 2015 1 4 23057.30 0.940 5 cohortGrowthselftest
## 243 2016 1 4 30705.80 0.497 5 cohortGrowthselftest
## 244 2017 1 4 45924.20 0.300 5 cohortGrowthselftest
## 245 2018 1 4 41260.60 0.670 5 cohortGrowthselftest
## 246 2019 1 4 36906.20 0.190 5 cohortGrowthselftest
## 247 1986 1 5 8131.22 0.600 5 cohortGrowthselftest
## 248 1987 1 5 2430.50 0.560 5 cohortGrowthselftest
## 249 1993 10 5 23324.90 0.290 5 cohortGrowthselftest
## 250 2003 10 5 58452.20 0.230 5 cohortGrowthselftest
## 251 2004 10 5 65035.40 0.550 5 cohortGrowthselftest
## 252 2006 10 5 109329.00 0.300 5 cohortGrowthselftest
## 253 2007 10 5 154467.00 0.270 5 cohortGrowthselftest
## 254 2008 10 5 68056.30 0.240 5 cohortGrowthselftest
## 255 2009 10 5 72360.30 0.400 5 cohortGrowthselftest
## 256 2010 10 5 44703.20 0.270 5 cohortGrowthselftest
## 257 2011 10 5 54234.90 0.270 5 cohortGrowthselftest
## 258 2012 10 5 32600.60 0.290 5 cohortGrowthselftest
## 259 2014 10 5 3775.21 0.540 5 cohortGrowthselftest
## 260 1986 1 6 18676.60 0.730 5 cohortGrowthselftest
## 261 1987 1 6 19940.10 0.480 5 cohortGrowthselftest
## 262 1987 10 6 29682.60 0.350 5 cohortGrowthselftest
## 263 1993 10 6 69470.00 0.210 5 cohortGrowthselftest
## 264 1995 10 6 392947.00 0.400 5 cohortGrowthselftest
## 265 1996 10 6 370045.00 0.210 5 cohortGrowthselftest
## 266 1997 10 6 546270.00 0.330 5 cohortGrowthselftest
## 267 1998 10 6 321022.00 0.340 5 cohortGrowthselftest
## 268 1999 10 6 633369.00 0.390 5 cohortGrowthselftest
## 269 2000 10 6 583315.00 0.380 5 cohortGrowthselftest
## 270 2001 10 6 418106.00 0.170 5 cohortGrowthselftest
## 271 2002 10 6 373917.00 0.180 5 cohortGrowthselftest
## 272 2003 10 6 253238.00 0.240 5 cohortGrowthselftest
## 273 2004 10 6 274313.00 0.400 5 cohortGrowthselftest
## 274 2005 10 6 434194.00 0.250 5 cohortGrowthselftest
## 275 2006 10 6 524170.00 0.260 5 cohortGrowthselftest
## 276 2007 10 6 281360.00 0.210 5 cohortGrowthselftest
## 277 2008 10 6 645590.00 0.220 5 cohortGrowthselftest
## 278 2009 10 6 540859.00 0.390 5 cohortGrowthselftest
## 279 2010 10 6 128197.00 0.260 5 cohortGrowthselftest
## 280 2011 10 6 169739.00 0.270 5 cohortGrowthselftest
## 281 2012 10 6 76649.00 0.290 5 cohortGrowthselftest
## 282 2014 10 6 22410.20 0.660 5 cohortGrowthselftest
## 283 2005 10 4 1715810.00 0.300 6 cohortGrowthselftest
## 284 2007 10 4 903193.00 0.090 6 cohortGrowthselftest
## 285 2009 10 4 566609.00 0.410 6 cohortGrowthselftest
## 286 2010 10 4 537752.00 0.300 6 cohortGrowthselftest
## 287 2011 10 4 269894.00 0.280 6 cohortGrowthselftest
## 288 2012 10 4 189472.00 0.240 6 cohortGrowthselftest
## 289 2013 10 4 57437.10 0.380 6 cohortGrowthselftest
## 290 2014 10 4 44603.00 0.290 6 cohortGrowthselftest
## 291 2015 10 4 64365.80 0.470 6 cohortGrowthselftest
## 292 2008 1 4 853675.00 0.300 6 cohortGrowthselftest
## 293 2012 1 4 342219.00 0.330 6 cohortGrowthselftest
## 294 2013 1 4 354352.00 0.293 6 cohortGrowthselftest
## 295 2014 1 4 204476.00 0.697 6 cohortGrowthselftest
## 296 2015 1 4 110309.00 0.940 6 cohortGrowthselftest
## 297 2016 1 4 27838.30 0.497 6 cohortGrowthselftest
## 298 2017 1 4 43216.30 0.300 6 cohortGrowthselftest
## 299 2018 1 4 41334.70 0.670 6 cohortGrowthselftest
## 300 2019 1 4 35617.50 0.190 6 cohortGrowthselftest
## 301 1986 1 5 8849.26 0.600 6 cohortGrowthselftest
## 302 1987 1 5 6175.15 0.560 6 cohortGrowthselftest
## 303 1993 10 5 36462.70 0.290 6 cohortGrowthselftest
## 304 2003 10 5 84163.10 0.230 6 cohortGrowthselftest
## 305 2004 10 5 129617.00 0.550 6 cohortGrowthselftest
## 306 2006 10 5 130025.00 0.300 6 cohortGrowthselftest
## 307 2007 10 5 178531.00 0.270 6 cohortGrowthselftest
## 308 2008 10 5 172268.00 0.240 6 cohortGrowthselftest
## 309 2009 10 5 102699.00 0.400 6 cohortGrowthselftest
## 310 2010 10 5 76853.40 0.270 6 cohortGrowthselftest
## 311 2011 10 5 59295.60 0.270 6 cohortGrowthselftest
## 312 2012 10 5 27173.80 0.290 6 cohortGrowthselftest
## 313 2014 10 5 8168.78 0.540 6 cohortGrowthselftest
## 314 1986 1 6 39912.50 0.730 6 cohortGrowthselftest
## 315 1987 1 6 24540.20 0.480 6 cohortGrowthselftest
## 316 1987 10 6 19631.60 0.350 6 cohortGrowthselftest
## 317 1993 10 6 116456.00 0.210 6 cohortGrowthselftest
## 318 1995 10 6 321291.00 0.400 6 cohortGrowthselftest
## 319 1996 10 6 265594.00 0.210 6 cohortGrowthselftest
## 320 1997 10 6 397998.00 0.330 6 cohortGrowthselftest
## 321 1998 10 6 539604.00 0.340 6 cohortGrowthselftest
## 322 1999 10 6 629355.00 0.390 6 cohortGrowthselftest
## 323 2000 10 6 543633.00 0.380 6 cohortGrowthselftest
## 324 2001 10 6 351253.00 0.170 6 cohortGrowthselftest
## 325 2002 10 6 401143.00 0.180 6 cohortGrowthselftest
## 326 2003 10 6 332752.00 0.240 6 cohortGrowthselftest
## 327 2004 10 6 434401.00 0.400 6 cohortGrowthselftest
## 328 2005 10 6 473800.00 0.250 6 cohortGrowthselftest
## 329 2006 10 6 509759.00 0.260 6 cohortGrowthselftest
## 330 2007 10 6 453935.00 0.210 6 cohortGrowthselftest
## 331 2008 10 6 437798.00 0.220 6 cohortGrowthselftest
## 332 2009 10 6 310228.00 0.390 6 cohortGrowthselftest
## 333 2010 10 6 237757.00 0.260 6 cohortGrowthselftest
## 334 2011 10 6 218337.00 0.270 6 cohortGrowthselftest
## 335 2012 10 6 97585.90 0.290 6 cohortGrowthselftest
## 336 2014 10 6 35344.20 0.660 6 cohortGrowthselftest
## 337 2005 10 4 809070.00 0.300 7 cohortGrowthselftest
## 338 2007 10 4 984829.00 0.090 7 cohortGrowthselftest
## 339 2009 10 4 617036.00 0.410 7 cohortGrowthselftest
## 340 2010 10 4 358310.00 0.300 7 cohortGrowthselftest
## 341 2011 10 4 504825.00 0.280 7 cohortGrowthselftest
## 342 2012 10 4 210589.00 0.240 7 cohortGrowthselftest
## 343 2013 10 4 68530.40 0.380 7 cohortGrowthselftest
## 344 2014 10 4 66526.00 0.290 7 cohortGrowthselftest
## 345 2015 10 4 17234.90 0.470 7 cohortGrowthselftest
## 346 2008 1 4 935789.00 0.300 7 cohortGrowthselftest
## 347 2012 1 4 435753.00 0.330 7 cohortGrowthselftest
## 348 2013 1 4 215050.00 0.293 7 cohortGrowthselftest
## 349 2014 1 4 174268.00 0.697 7 cohortGrowthselftest
## 350 2015 1 4 78982.30 0.940 7 cohortGrowthselftest
## 351 2016 1 4 11955.70 0.497 7 cohortGrowthselftest
## 352 2017 1 4 39469.00 0.300 7 cohortGrowthselftest
## 353 2018 1 4 28599.00 0.670 7 cohortGrowthselftest
## 354 2019 1 4 39239.40 0.190 7 cohortGrowthselftest
## 355 1986 1 5 3224.00 0.600 7 cohortGrowthselftest
## 356 1987 1 5 2087.72 0.560 7 cohortGrowthselftest
## 357 1993 10 5 38552.60 0.290 7 cohortGrowthselftest
## 358 2003 10 5 85270.50 0.230 7 cohortGrowthselftest
## 359 2004 10 5 71704.70 0.550 7 cohortGrowthselftest
## 360 2006 10 5 134151.00 0.300 7 cohortGrowthselftest
## 361 2007 10 5 110034.00 0.270 7 cohortGrowthselftest
## 362 2008 10 5 136620.00 0.240 7 cohortGrowthselftest
## 363 2009 10 5 73130.20 0.400 7 cohortGrowthselftest
## 364 2010 10 5 50762.20 0.270 7 cohortGrowthselftest
## 365 2011 10 5 50474.00 0.270 7 cohortGrowthselftest
## 366 2012 10 5 34888.30 0.290 7 cohortGrowthselftest
## 367 2014 10 5 6286.22 0.540 7 cohortGrowthselftest
## 368 1986 1 6 20503.00 0.730 7 cohortGrowthselftest
## 369 1987 1 6 27461.90 0.480 7 cohortGrowthselftest
## 370 1987 10 6 35026.90 0.350 7 cohortGrowthselftest
## 371 1993 10 6 131919.00 0.210 7 cohortGrowthselftest
## 372 1995 10 6 212092.00 0.400 7 cohortGrowthselftest
## 373 1996 10 6 487677.00 0.210 7 cohortGrowthselftest
## 374 1997 10 6 425824.00 0.330 7 cohortGrowthselftest
## 375 1998 10 6 1454620.00 0.340 7 cohortGrowthselftest
## 376 1999 10 6 756531.00 0.390 7 cohortGrowthselftest
## 377 2000 10 6 1140470.00 0.380 7 cohortGrowthselftest
## 378 2001 10 6 406106.00 0.170 7 cohortGrowthselftest
## 379 2002 10 6 323548.00 0.180 7 cohortGrowthselftest
## 380 2003 10 6 455874.00 0.240 7 cohortGrowthselftest
## 381 2004 10 6 169939.00 0.400 7 cohortGrowthselftest
## 382 2005 10 6 390169.00 0.250 7 cohortGrowthselftest
## 383 2006 10 6 721717.00 0.260 7 cohortGrowthselftest
## 384 2007 10 6 259102.00 0.210 7 cohortGrowthselftest
## 385 2008 10 6 330947.00 0.220 7 cohortGrowthselftest
## 386 2009 10 6 171863.00 0.390 7 cohortGrowthselftest
## 387 2010 10 6 233285.00 0.260 7 cohortGrowthselftest
## 388 2011 10 6 205884.00 0.270 7 cohortGrowthselftest
## 389 2012 10 6 92035.90 0.290 7 cohortGrowthselftest
## 390 2014 10 6 28706.70 0.660 7 cohortGrowthselftest
## 391 2005 10 4 1175170.00 0.300 8 cohortGrowthselftest
## 392 2007 10 4 874505.00 0.090 8 cohortGrowthselftest
## 393 2009 10 4 257698.00 0.410 8 cohortGrowthselftest
## 394 2010 10 4 483967.00 0.300 8 cohortGrowthselftest
## 395 2011 10 4 379795.00 0.280 8 cohortGrowthselftest
## 396 2012 10 4 235197.00 0.240 8 cohortGrowthselftest
## 397 2013 10 4 129553.00 0.380 8 cohortGrowthselftest
## 398 2014 10 4 31636.20 0.290 8 cohortGrowthselftest
## 399 2015 10 4 19465.10 0.470 8 cohortGrowthselftest
## 400 2008 1 4 624801.00 0.300 8 cohortGrowthselftest
## 401 2012 1 4 254300.00 0.330 8 cohortGrowthselftest
## 402 2013 1 4 206454.00 0.293 8 cohortGrowthselftest
## 403 2014 1 4 85902.50 0.697 8 cohortGrowthselftest
## 404 2015 1 4 63890.80 0.940 8 cohortGrowthselftest
## 405 2016 1 4 106199.00 0.497 8 cohortGrowthselftest
## 406 2017 1 4 46967.50 0.300 8 cohortGrowthselftest
## 407 2018 1 4 23569.10 0.670 8 cohortGrowthselftest
## 408 2019 1 4 36855.80 0.190 8 cohortGrowthselftest
## 409 1986 1 5 3709.67 0.600 8 cohortGrowthselftest
## 410 1987 1 5 5505.26 0.560 8 cohortGrowthselftest
## 411 1993 10 5 30049.40 0.290 8 cohortGrowthselftest
## 412 2003 10 5 66770.20 0.230 8 cohortGrowthselftest
## 413 2004 10 5 80911.40 0.550 8 cohortGrowthselftest
## 414 2006 10 5 272475.00 0.300 8 cohortGrowthselftest
## 415 2007 10 5 171586.00 0.270 8 cohortGrowthselftest
## 416 2008 10 5 120646.00 0.240 8 cohortGrowthselftest
## 417 2009 10 5 55773.00 0.400 8 cohortGrowthselftest
## 418 2010 10 5 64527.60 0.270 8 cohortGrowthselftest
## 419 2011 10 5 83034.30 0.270 8 cohortGrowthselftest
## 420 2012 10 5 31008.00 0.290 8 cohortGrowthselftest
## 421 2014 10 5 4191.42 0.540 8 cohortGrowthselftest
## 422 1986 1 6 44622.10 0.730 8 cohortGrowthselftest
## 423 1987 1 6 14814.80 0.480 8 cohortGrowthselftest
## 424 1987 10 6 48390.80 0.350 8 cohortGrowthselftest
## 425 1993 10 6 89041.90 0.210 8 cohortGrowthselftest
## 426 1995 10 6 331478.00 0.400 8 cohortGrowthselftest
## 427 1996 10 6 449873.00 0.210 8 cohortGrowthselftest
## 428 1997 10 6 558446.00 0.330 8 cohortGrowthselftest
## 429 1998 10 6 831350.00 0.340 8 cohortGrowthselftest
## 430 1999 10 6 552492.00 0.390 8 cohortGrowthselftest
## 431 2000 10 6 341350.00 0.380 8 cohortGrowthselftest
## 432 2001 10 6 511001.00 0.170 8 cohortGrowthselftest
## 433 2002 10 6 331949.00 0.180 8 cohortGrowthselftest
## 434 2003 10 6 235632.00 0.240 8 cohortGrowthselftest
## 435 2004 10 6 233135.00 0.400 8 cohortGrowthselftest
## 436 2005 10 6 396254.00 0.250 8 cohortGrowthselftest
## 437 2006 10 6 290096.00 0.260 8 cohortGrowthselftest
## 438 2007 10 6 474052.00 0.210 8 cohortGrowthselftest
## 439 2008 10 6 459917.00 0.220 8 cohortGrowthselftest
## 440 2009 10 6 232746.00 0.390 8 cohortGrowthselftest
## 441 2010 10 6 218156.00 0.260 8 cohortGrowthselftest
## 442 2011 10 6 217456.00 0.270 8 cohortGrowthselftest
## 443 2012 10 6 179588.00 0.290 8 cohortGrowthselftest
## 444 2014 10 6 25992.60 0.660 8 cohortGrowthselftest
## 445 2005 10 4 1852970.00 0.300 9 cohortGrowthselftest
## 446 2007 10 4 921944.00 0.090 9 cohortGrowthselftest
## 447 2009 10 4 900777.00 0.410 9 cohortGrowthselftest
## 448 2010 10 4 401490.00 0.300 9 cohortGrowthselftest
## 449 2011 10 4 303678.00 0.280 9 cohortGrowthselftest
## 450 2012 10 4 278312.00 0.240 9 cohortGrowthselftest
## 451 2013 10 4 75216.90 0.380 9 cohortGrowthselftest
## 452 2014 10 4 37193.10 0.290 9 cohortGrowthselftest
## 453 2015 10 4 28392.80 0.470 9 cohortGrowthselftest
## 454 2008 1 4 835181.00 0.300 9 cohortGrowthselftest
## 455 2012 1 4 327496.00 0.330 9 cohortGrowthselftest
## 456 2013 1 4 116319.00 0.293 9 cohortGrowthselftest
## 457 2014 1 4 72099.10 0.697 9 cohortGrowthselftest
## 458 2015 1 4 14457.10 0.940 9 cohortGrowthselftest
## 459 2016 1 4 45758.70 0.497 9 cohortGrowthselftest
## 460 2017 1 4 49649.20 0.300 9 cohortGrowthselftest
## 461 2018 1 4 25492.20 0.670 9 cohortGrowthselftest
## 462 2019 1 4 35059.30 0.190 9 cohortGrowthselftest
## 463 1986 1 5 13631.90 0.600 9 cohortGrowthselftest
## 464 1987 1 5 2708.64 0.560 9 cohortGrowthselftest
## 465 1993 10 5 34501.40 0.290 9 cohortGrowthselftest
## 466 2003 10 5 85930.50 0.230 9 cohortGrowthselftest
## 467 2004 10 5 131636.00 0.550 9 cohortGrowthselftest
## 468 2006 10 5 151099.00 0.300 9 cohortGrowthselftest
## 469 2007 10 5 109194.00 0.270 9 cohortGrowthselftest
## 470 2008 10 5 150091.00 0.240 9 cohortGrowthselftest
## 471 2009 10 5 112830.00 0.400 9 cohortGrowthselftest
## 472 2010 10 5 48127.70 0.270 9 cohortGrowthselftest
## 473 2011 10 5 50786.80 0.270 9 cohortGrowthselftest
## 474 2012 10 5 26183.50 0.290 9 cohortGrowthselftest
## 475 2014 10 5 19361.40 0.540 9 cohortGrowthselftest
## 476 1986 1 6 35177.70 0.730 9 cohortGrowthselftest
## 477 1987 1 6 20273.00 0.480 9 cohortGrowthselftest
## 478 1987 10 6 22073.00 0.350 9 cohortGrowthselftest
## 479 1993 10 6 97742.70 0.210 9 cohortGrowthselftest
## 480 1995 10 6 190614.00 0.400 9 cohortGrowthselftest
## 481 1996 10 6 586025.00 0.210 9 cohortGrowthselftest
## 482 1997 10 6 416900.00 0.330 9 cohortGrowthselftest
## 483 1998 10 6 480223.00 0.340 9 cohortGrowthselftest
## 484 1999 10 6 699698.00 0.390 9 cohortGrowthselftest
## 485 2000 10 6 348349.00 0.380 9 cohortGrowthselftest
## 486 2001 10 6 516666.00 0.170 9 cohortGrowthselftest
## 487 2002 10 6 328623.00 0.180 9 cohortGrowthselftest
## 488 2003 10 6 280141.00 0.240 9 cohortGrowthselftest
## 489 2004 10 6 276025.00 0.400 9 cohortGrowthselftest
## 490 2005 10 6 254271.00 0.250 9 cohortGrowthselftest
## 491 2006 10 6 476442.00 0.260 9 cohortGrowthselftest
## 492 2007 10 6 544301.00 0.210 9 cohortGrowthselftest
## 493 2008 10 6 290753.00 0.220 9 cohortGrowthselftest
## 494 2009 10 6 215718.00 0.390 9 cohortGrowthselftest
## 495 2010 10 6 388838.00 0.260 9 cohortGrowthselftest
## 496 2011 10 6 223064.00 0.270 9 cohortGrowthselftest
## 497 2012 10 6 134823.00 0.290 9 cohortGrowthselftest
## 498 2014 10 6 97158.10 0.660 9 cohortGrowthselftest
## model_run
## 1 historical_values
## 2 historical_values
## 3 historical_values
## 4 historical_values
## 5 historical_values
## 6 historical_values
## 7 historical_values
## 8 historical_values
## 9 historical_values
## 10 historical_values
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## 30 historical_values
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## 57 historical_values
## 58 historical_values
## 59 historical_values
## 60 historical_values
## 61 OM_expected_values
## 62 OM_expected_values
## 63 OM_expected_values
## 64 OM_expected_values
## 65 OM_expected_values
## 66 OM_expected_values
## 67 OM_expected_values
## 68 OM_expected_values
## 69 OM_expected_values
## 70 OM_expected_values
## 71 OM_expected_values
## 72 OM_expected_values
## 73 OM_expected_values
## 74 OM_expected_values
## 75 OM_expected_values
## 76 OM_expected_values
## 77 OM_expected_values
## 78 OM_expected_values
## 85 OM_expected_values
## 86 OM_expected_values
## 87 OM_expected_values
## 88 OM_expected_values
## 89 OM_expected_values
## 90 OM_expected_values
## 91 OM_expected_values
## 92 OM_expected_values
## 93 OM_expected_values
## 94 OM_expected_values
## 95 OM_expected_values
## 96 OM_expected_values
## 97 OM_expected_values
## 98 OM_expected_values
## 99 OM_expected_values
## 100 OM_expected_values
## 101 OM_expected_values
## 102 OM_expected_values
## 103 OM_expected_values
## 104 OM_expected_values
## 105 OM_expected_values
## 106 OM_expected_values
## 107 OM_expected_values
## 108 OM_expected_values
## 109 OM_expected_values
## 110 OM_expected_values
## 111 OM_expected_values
## 112 OM_expected_values
## 113 OM_expected_values
## 114 OM_expected_values
## 115 OM_expected_values
## 116 OM_expected_values
## 117 OM_expected_values
## 118 OM_expected_values
## 119 OM_expected_values
## 120 OM_expected_values
## 121 sampled_dataset
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##
## $index_plot
Summary plots of terminal year estimates
termYr <- tsSumry %>% filter(model_run %in% c("0_estimate_cohort_growh_OM",
"cohortGrowthOMandEM_EM_init") | # or keep end years
year == as.numeric(regmatches(model_run,
gregexpr("[[:digit:]]+", model_run))))
termYr <- termYr %>% mutate(model_run = as.character(model_run),
model_run = case_when(!model_run %in% c("0_estimate_cohort_growh_OM",
"cohortGrowthOMandEM_EM_init") ~"cohortGrowthOMandEM_EM_term",
TRUE ~ model_run))
ggplot2::ggplot(data = termYr,
ggplot2::aes(x = year, y = SpawnBio)) +
ggplot2::geom_vline(xintercept = 2019, color = "gray") +
geom_point(data = simDat, mapping = aes(x = year, y = obs), shape = 4, color = "grey") +
ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = model_run))+
ggplot2::scale_color_manual(values = c("#D65F00", "black", rep("blue", 5))) +
ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
ggplot2::guides(linetype = FALSE) +
ggplot2::facet_wrap(. ~ iteration) +
ggplot2::theme_classic()## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
relSSB_EMtoOM <- termYr %>% select(model_run, year, iteration, SpawnBio) %>%
pivot_wider(id_cols = c(year, iteration),
names_from = model_run, values_from = SpawnBio) %>%
rename(cohort_growth_OM = "0_estimate_cohort_growh_OM") %>%
mutate(diffSSB = case_when(is.na(cohortGrowthOMandEM_EM_term) ~ cohortGrowthOMandEM_EM_init - cohort_growth_OM,
!is.na(cohortGrowthOMandEM_EM_term) ~ cohortGrowthOMandEM_EM_term - cohort_growth_OM))
relSSB_EMtoOM <- relSSB_EMtoOM %>% full_join(y = simDat, by = c("year", "iteration")) %>%
mutate(diffDat = obs - cohort_growth_OM)
ggplot(data = relSSB_EMtoOM, aes(x = year, y = diffSSB)) +
ggplot2::geom_vline(xintercept = 2019, color = "gray") +
geom_hline(yintercept = 0, color = "black") +
geom_point(mapping = aes(x = year, y = diffDat), shape = 4, color = "grey") +
ggplot2::geom_line(ggplot2::aes(linetype = as.character(iteration), color = 2))+
#ggplot2::scale_color_manual(values = c("#D65F00", "black", rep("blue", 5))) +
ggplot2::scale_linetype_manual(values = rep("solid", 50)) +
ggplot2::guides(linetype = FALSE) +
ggplot2::facet_wrap(. ~ iteration) +
ggplot2::theme_classic()## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## Warning: Removed 182 rows containing missing values (geom_point).## Warning: Removed 7 row(s) containing missing values (geom_path).
Plots of length and age composition
# plot_comp_sampling(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest", comp_type = "agecomp")
# !!!Error: The comp database from the operating model has no rows, so must not have been any historical data in the OM.
outputSS <- SS_output(
dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024",
dir.mcmc = NULL,
repfile = "Report.sso",
compfile = "CompReport.sso")## Getting header info from:
## C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/Report.sso## This function tested on SS versions 3.24 and 3.30.
## You are using 3.30.16.00 which SHOULD work with this package.## Report file time:Wed Jul 21 10:33:46 2021## Warning in SS_output(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Reading full report file## Got all columns using ncols = 62## Got Report file## Setting minimum biomass threshhold to 0.25 based on US west coast assumption associated with biomass target of 0.4. (can replace or override in SS_plots by setting 'minbthresh')## No non-empty log file in directory or too many files matching pattern *.log## Got warning file. Therewere 8 warnings in C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/warning.sso## Finished reading files## CompReport file separated by this code as follows (rows = Ncomps*Nbins):
## 3510 rows of length comp data,
## 0 rows of generalized size comp data,
## 0 rows of age comp data,
## 8991 rows of conditional age-at-length data,
## 783 rows of ghost fleet age comp data,
## 0 rows of ghost fleet conditional age-at-length data,
## 468 rows of ghost fleet length comp data,
## 0 rows of mean length at age data,
## 0 rows of mean weight at age data,
## 0 rows of 'TAG1' comp data, and
## 0 rows of 'TAG2' comp data.## Finished dimensioning## You skipped the covar file## Finished primary run statistics list##
## Statistics shown below (to turn off, change input to printstats=FALSE)## $SS_version
## [1] "3.30.16.00;_2020_09_03;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.2"
##
## $SS_versionshort
## [1] "3.30"
##
## $SS_versionNumeric
## [1] 3.3
##
## $StartTime
## [1] "StartTime: Wed Jul 21 10:33:46 2021"
##
## $RunTime
## [1] "0 hours, 5 minutes, 13 seconds."
##
## $Files_used
## [1] "Data_File: init_dat.ss Control_File: control.ss"
##
## $Nwarnings
## [1] 8
##
## $warnings
## [1] "#V3.30.16.00;_2020_09_03;_safe;_Stock_Synthesis_by_Richard_Methot_(NOAA)_using_ADMB_12.2"
## [2] "#Stock Synthesis (SS) is a work of the U.S. Government and is not subject to copyright protection in the United States."
## [3] "#Foreign copyrights may apply. See copyright.txt for more information."
## [4] "Wed Jul 21 10:33:45 2021"
## [5] ""
## [6] "settle_month is less than spawn_month, so logical age at settlement calculated to be: 1 for settle_time 1. Does not match read value of 0 are you sure? "
## [7] "setting in starter does not request all priors, and 5 parameters have priors and are not estimated, so their prior not included in obj_fun."
## [8] "Final gradient: 0.00238829 is larger than final_conv: 1e-05"
## [9] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1987 -10 15 8.36935 17.7371"
## [10] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1988 -10 15 8.36935 17.7371"
## [11] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1987 -10 15 8.36935 17.7371"
## [12] " adjusted selparm out of base parm bounds (Phase, Iter, Parm#, yr, min, max, base, value) 6 967 13 1988 -10 15 8.36935 17.7371"
## [13] "Number_of_active_parameters_on_or_near_bounds: 3"
## [14] " N warnings: 8"
##
## $likelihoods_used
## values lambdas
## TOTAL 1999.2400000 NA
## Catch 0.0169003 NA
## Equil_catch 0.0000000 NA
## Survey -31.1208000 NA
## Length_comp 1016.9500000 NA
## Age_comp 906.1670000 NA
## Recruitment 23.9418000 1
## InitEQ_Regime 0.0000000 0
## Forecast_Recruitment 0.1936790 1
## Parm_priors 0.0000000 1
## Parm_softbounds 0.0510629 NA
## Parm_devs 83.0382000 1
## Crash_Pen 0.0000000 1
##
## $likelihoods_laplace
## values lambdas
## NoBias_corr_Recruitment(info_only) 23.9418 1
## Laplace_obj_fun(info_only) 1999.2400 NA
##
## $likelihoods_by_fleet
## Label ALL MexCal_S1 MexCal_S2 PNW AT_Survey
## 180 Catch_lambda NA 1.0000000 1.00000e+00 1.00000e+00 1.00000
## 181 Catch_like 0.0169003 0.0168907 2.46461e-11 9.67905e-06 0.00000
## 182 Init_equ_lambda NA 0.0000000 0.00000e+00 0.00000e+00 1.00000
## 183 Init_equ_like 0.0000000 0.0000000 0.00000e+00 0.00000e+00 0.00000
## 184 Surv_lambda NA 0.0000000 0.00000e+00 0.00000e+00 1.00000
## 185 Surv_like -31.1208000 0.0000000 0.00000e+00 0.00000e+00 -7.27937
## 186 Surv_N_use NA 0.0000000 0.00000e+00 0.00000e+00 23.00000
## 187 Surv_N_skip NA 0.0000000 0.00000e+00 0.00000e+00 0.00000
## 188 Length_lambda NA 1.0000000 1.00000e+00 1.00000e+00 1.00000
## 189 Length_like 1016.9500000 278.7870000 4.59803e+02 1.63591e+02 114.77400
## 190 Length_N_use NA 30.0000000 3.40000e+01 1.70000e+01 9.00000
## 191 Length_N_skip NA 0.0000000 0.00000e+00 1.20000e+01 0.00000
## 192 Age_lambda NA 1.0000000 1.00000e+00 1.00000e+00 1.00000
## 193 Age_like 906.1670000 193.7000000 3.64017e+02 2.12135e+02 136.31600
## 194 Age_N_use NA 289.0000000 4.41000e+02 1.63000e+02 106.00000
## 195 Age_N_skip NA 29.0000000 3.30000e+01 1.60000e+01 9.00000
## DEPM TEP_all
## 180 1.00000 1.0000
## 181 0.00000 0.0000
## 182 1.00000 1.0000
## 183 0.00000 0.0000
## 184 1.00000 1.0000
## 185 -8.20715 -15.6342
## 186 13.00000 23.0000
## 187 0.00000 0.0000
## 188 0.00000 0.0000
## 189 0.00000 0.0000
## 190 0.00000 0.0000
## 191 0.00000 0.0000
## 192 0.00000 0.0000
## 193 0.00000 0.0000
## 194 0.00000 0.0000
## 195 0.00000 0.0000
##
## $Parm_devs_detail
## Index Phase MinYr MaxYr stddev Rho Like_devs Like_se mean rmse
## 199 1 4 1982 2019 0.01 0 18.0323 0 -0.0158261 0.974201
## 200 2 5 1982 2019 0.11 0 65.0059 0 -0.5356730 1.849690
##
## $N_estimated_parameters
## [1] 275
##
## $table_of_phases
##
## -99 -6 -5 -4 -3 -2 -1 1 2 3 4 5 6
## 1 2 3 2 10 4 3 38 6 130 56 38 7
##
## $estimated_non_dev_parameters
## Value Phase Min Max
## L_at_Amin_Fem_GP_1 10.132700000 3 3.00 30.00
## L_at_Amax_Fem_GP_1 23.326300000 3 15.00 40.00
## VonBert_K_Fem_GP_1 0.616584000 3 0.05 0.99
## CV_young_Fem_GP_1 0.180989000 3 0.05 0.50
## CV_old_Fem_GP_1 0.041245700 3 0.01 0.10
## SR_LN(R0) 16.322700000 1 3.00 25.00
## SR_regime_BLK1repl_1980 -4.760540000 4 -15.00 15.00
## InitF_seas_2_flt_2MexCal_S2 5.001860000 1 0.00 14.00
## Size_inflection_MexCal_S1(1) 13.560500000 3 0.00 30.00
## Size_95%width_MexCal_S1(1) 1.975260000 3 0.00 10.00
## AgeSel_P1_MexCal_S1(1) 0.498526000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1) 0.501577000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1) 10.028700000 3 -10.00 15.00
## AgeSel_P4_MexCal_S1(1) 0.794342000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1) -1.388510000 3 -10.00 11.00
## AgeSel_P6_MexCal_S1(1) 0.610979000 3 -10.00 11.00
## AgeSel_P7_MexCal_S1(1) -1.140710000 3 -10.00 11.00
## AgeSel_P8_MexCal_S1(1) -1.241410000 3 -10.00 11.00
## AgeSel_P9_MexCal_S1(1) -5.816460000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2) 8.369350000 3 -10.00 15.00
## AgeSel_P3_MexCal_S2(2) 1.759270000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2) 0.268068000 3 -10.00 11.00
## AgeSel_P5_MexCal_S2(2) -0.793967000 3 -10.00 11.00
## AgeSel_P6_MexCal_S2(2) 0.411625000 3 -10.00 11.00
## AgeSel_P7_MexCal_S2(2) -1.233660000 3 -10.00 11.00
## AgeSel_P8_MexCal_S2(2) -0.217423000 3 -10.00 11.00
## AgeSel_P9_MexCal_S2(2) -1.920890000 3 -10.00 11.00
## Age_inflection_PNW(3) 9.798310000 4 0.00 10.00
## Age_95%width_PNW(3) 1.168340000 4 -5.00 15.00
## AgeSel_P2_AT_Survey(4) 1.146160000 4 0.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983 4.380830000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985 4.391080000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987 5.827630000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989 2.918220000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991 0.504110000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993 5.578460000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 -2.538470000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 -1.156910000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999 -4.582480000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001 -3.100720000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003 -2.225720000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005 -2.350380000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007 -3.355650000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009 6.551200000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011 3.735560000 3 -10.00 11.00
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013 -4.721470000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.375324000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 1.044390000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987 0.065048600 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 1.432350000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 11.805200000 3 -10.00 15.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -1.101940000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995 2.165550000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 -0.081507300 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 0.862265000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 -0.741943000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 -1.277650000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 -1.301360000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007 0.576038000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009 0.009128510 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011 0.411197000 3 -10.00 11.00
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013 0.345985000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -6.791940000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 -6.577600000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 -2.003120000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 3.262670000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991 2.089600000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 2.019210000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995 1.330810000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 -0.759134000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 -1.015490000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001 0.046350400 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 -0.527423000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 -0.166169000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 -1.451590000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 -0.853352000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011 1.089490000 3 -10.00 11.00
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.360910000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983 -1.887870000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985 -1.419030000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987 3.096990000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 -7.129140000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991 0.171356000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 -7.113480000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 -4.154440000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997 -0.474855000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999 -1.364360000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001 -3.152860000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003 -0.663141000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 -1.515550000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007 -6.377660000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009 -4.068960000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011 -1.662910000 3 -10.00 11.00
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013 1.768640000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987 9.367740000 3 -10.00 15.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989 -6.529080000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991 -7.965270000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993 -7.817700000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995 -8.815180000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997 -7.937600000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999 -8.963000000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001 -9.838380000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003 -7.858780000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005 -8.985060000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007 -8.773230000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009 -8.321650000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011 -9.977730000 3 -10.00 11.00
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013 -5.785790000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987 -0.396588000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989 -2.070610000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991 -1.206140000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993 -2.305950000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995 -0.945957000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997 -2.031790000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999 -1.858030000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001 -1.818520000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003 -2.647180000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005 -3.004590000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007 -2.729860000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009 -4.279050000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011 -0.880619000 3 -10.00 11.00
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013 -0.975195000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987 -0.224743000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989 1.293600000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991 0.811333000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993 -1.221430000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995 -1.400710000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997 -0.099285200 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999 -2.149930000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001 -1.676120000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003 -0.003437220 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005 -0.845493000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007 -1.854010000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009 -0.217583000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011 -0.045884000 3 -10.00 11.00
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013 -0.942944000 3 -10.00 11.00
## Age_inflection_PNW(3)_BLK4repl_1999 2.524920000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2001 2.625380000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2003 1.912140000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2005 2.806140000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2007 3.711570000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2009 3.978920000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2011 2.560110000 4 0.00 10.00
## Age_inflection_PNW(3)_BLK4repl_2013 3.275700000 4 0.00 10.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012 7.402270000 4 0.00 9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013 7.856880000 4 0.00 9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014 0.944888000 4 0.00 9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016 8.057620000 4 0.00 9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018 0.000444865 4 0.00 9.00
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019 9.845330000 4 0.00 11.00
## Init Status Parm_StDev
## L_at_Amin_Fem_GP_1 8.000000000 OK 0
## L_at_Amax_Fem_GP_1 26.719900000 OK 0
## VonBert_K_Fem_GP_1 0.721427000 OK 0
## CV_young_Fem_GP_1 0.164739000 OK 0
## CV_old_Fem_GP_1 0.039694500 OK 0
## SR_LN(R0) 15.351600000 OK 0
## SR_regime_BLK1repl_1980 -2.254580000 OK 0
## InitF_seas_2_flt_2MexCal_S2 10.000000000 OK 0
## Size_inflection_MexCal_S1(1) 14.004200000 OK 0
## Size_95%width_MexCal_S1(1) 2.002900000 OK 0
## AgeSel_P1_MexCal_S1(1) 1.000040000 OK 0
## AgeSel_P2_MexCal_S1(1) 0.837451000 OK 0
## AgeSel_P3_MexCal_S1(1) -0.884887000 OK 0
## AgeSel_P4_MexCal_S1(1) -0.635305000 OK 0
## AgeSel_P5_MexCal_S1(1) 0.918160000 OK 0
## AgeSel_P6_MexCal_S1(1) -0.111484000 OK 0
## AgeSel_P7_MexCal_S1(1) -0.989063000 OK 0
## AgeSel_P8_MexCal_S1(1) -1.493050000 OK 0
## AgeSel_P9_MexCal_S1(1) -1.895360000 OK 0
## AgeSel_P2_MexCal_S2(2) 0.769735000 OK 0
## AgeSel_P3_MexCal_S2(2) 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2) -0.104782000 OK 0
## AgeSel_P5_MexCal_S2(2) -1.034120000 OK 0
## AgeSel_P6_MexCal_S2(2) 0.213999000 OK 0
## AgeSel_P7_MexCal_S2(2) -1.773900000 OK 0
## AgeSel_P8_MexCal_S2(2) -0.285435000 OK 0
## AgeSel_P9_MexCal_S2(2) -6.978780000 OK 0
## Age_inflection_PNW(3) 5.000950000 OK 0
## Age_95%width_PNW(3) 0.483799000 OK 0
## AgeSel_P2_AT_Survey(4) 0.000433815 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011 0.837451000 OK 0
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013 0.837451000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011 -0.884887000 OK 0
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013 -0.884887000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011 -0.635305000 OK 0
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.635305000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011 0.918160000 OK 0
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013 0.918160000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001 0.769735000 LO 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009 0.769735000 OK 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011 0.769735000 LO 0
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013 0.769735000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011 0.135819000 OK 0
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011 0.135819000 OK 0
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013 0.135819000 OK 0
## Age_inflection_PNW(3)_BLK4repl_1999 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2001 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2003 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2005 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2007 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2009 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2011 5.000950000 OK 0
## Age_inflection_PNW(3)_BLK4repl_2013 5.000950000 OK 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012 0.000433815 OK 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013 0.000433815 OK 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014 0.000433815 OK 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016 0.000433815 OK 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018 0.000433815 LO 0
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019 0.000433815 OK 0
## Gradient Pr_type Prior Pr_SD
## L_at_Amin_Fem_GP_1 0.0004129400000 No_prior NA NA
## L_at_Amax_Fem_GP_1 0.0003641360000 No_prior NA NA
## VonBert_K_Fem_GP_1 0.0001858540000 No_prior NA NA
## CV_young_Fem_GP_1 0.0000552808000 No_prior NA NA
## CV_old_Fem_GP_1 0.0000248393000 No_prior NA NA
## SR_LN(R0) 0.0023882900000 No_prior NA NA
## SR_regime_BLK1repl_1980 0.0007875360000 No_prior NA NA
## InitF_seas_2_flt_2MexCal_S2 -0.0000261434000 No_prior NA NA
## Size_inflection_MexCal_S1(1) 0.0000460351000 No_prior NA NA
## Size_95%width_MexCal_S1(1) 0.0000252338000 No_prior NA NA
## AgeSel_P1_MexCal_S1(1) -0.0000004409960 No_prior NA NA
## AgeSel_P2_MexCal_S1(1) -0.0000002487060 No_prior NA NA
## AgeSel_P3_MexCal_S1(1) 0.0000002844490 No_prior NA NA
## AgeSel_P4_MexCal_S1(1) 0.0000184525000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1) -0.0000017911000 No_prior NA NA
## AgeSel_P6_MexCal_S1(1) 0.0000582053000 No_prior NA NA
## AgeSel_P7_MexCal_S1(1) 0.0000115176000 No_prior NA NA
## AgeSel_P8_MexCal_S1(1) 0.0000050345500 No_prior NA NA
## AgeSel_P9_MexCal_S1(1) -0.0000010454100 No_prior NA NA
## AgeSel_P2_MexCal_S2(2) 0.0000752276000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2) 0.0000779974000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2) 0.0000552218000 No_prior NA NA
## AgeSel_P5_MexCal_S2(2) 0.0000582164000 No_prior NA NA
## AgeSel_P6_MexCal_S2(2) 0.0001039840000 No_prior NA NA
## AgeSel_P7_MexCal_S2(2) 0.0001265330000 No_prior NA NA
## AgeSel_P8_MexCal_S2(2) -0.0000093906300 No_prior NA NA
## AgeSel_P9_MexCal_S2(2) 0.0000032698200 No_prior NA NA
## Age_inflection_PNW(3) 0.0000097495200 No_prior NA NA
## Age_95%width_PNW(3) -0.0000574965000 No_prior NA NA
## AgeSel_P2_AT_Survey(4) -0.0000018101200 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983 -0.0000004753150 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985 -0.0000004489450 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987 -0.0000004658210 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989 -0.0000007346270 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991 0.0000004124690 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993 -0.0000000743509 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 -0.0000067762900 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 -0.0000035103600 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999 0.0003424160000 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001 0.0002928440000 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003 0.0000030969400 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005 0.0000156595000 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007 0.0001062260000 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009 0.0000001089530 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011 -0.0000000100571 No_prior NA NA
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013 0.0000032174100 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 -0.0000114249000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 -0.0000026537000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987 0.0000132896000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 -0.0000004882750 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 0.0000000213025 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 -0.0000079205500 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995 0.0000068543200 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 0.0000184488000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 0.0003720230000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 0.0001919990000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 0.0000095309500 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 0.0000168828000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007 0.0001017960000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009 0.0000232025000 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011 0.0000023466900 No_prior NA NA
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013 0.0000041264500 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 -0.0000003705730 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 0.0000000278957 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 0.0000184008000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 -0.0000010338500 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991 0.0000003182380 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 -0.0000029134700 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995 0.0000339261000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 0.0000268911000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 0.0000919447000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001 0.0001267910000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 0.0000173136000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 0.0000152684000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 0.0000336254000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 0.0000349591000 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011 0.0000017603500 No_prior NA NA
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 -0.0000036137100 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983 0.0000011660300 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985 0.0000007834760 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987 0.0000163781000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 -0.0000000621945 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991 -0.0000030903100 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 -0.0000003400530 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 -0.0000084814300 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997 0.0000160585000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999 0.0000267475000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001 0.0000368947000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003 0.0000113444000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 -0.0000044314700 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007 0.0000006995080 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009 0.0000006160660 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011 0.0000151818000 No_prior NA NA
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013 0.0000048618900 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987 -0.0000005176920 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989 -0.0000052980600 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991 0.0000370974000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993 0.0000017766200 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995 0.0000133862000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997 -0.0000018761500 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999 0.0000073162300 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001 0.0000218295000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003 0.0000213894000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005 0.0000121440000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007 -0.0000137342000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009 -0.0000722672000 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011 0.0000003970010 No_prior NA NA
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013 0.0000112483000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987 -0.0000106226000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989 0.0000228550000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991 0.0001138560000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993 0.0000180892000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995 0.0000194009000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997 0.0000019083700 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999 0.0000034075200 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001 0.0000201722000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003 0.0000114949000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005 0.0000014433000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007 -0.0000091310600 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009 -0.0000746595000 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011 0.0000049297700 No_prior NA NA
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013 -0.0000024032300 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987 -0.0000499170000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989 -0.0000113576000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991 0.0000739941000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993 0.0000007493920 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995 0.0000050113600 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997 -0.0000024915200 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999 -0.0000002018530 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001 0.0000043343500 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003 0.0000101805000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005 -0.0000151087000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007 -0.0000112271000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009 -0.0000986508000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011 0.0000218388000 No_prior NA NA
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013 -0.0000215378000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_1999 0.0000181743000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2001 0.0000164624000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2003 0.0000060034900 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2005 0.0000206243000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2007 0.0000005837640 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2009 -0.0000105866000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2011 -0.0000100990000 No_prior NA NA
## Age_inflection_PNW(3)_BLK4repl_2013 -0.0000289703000 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012 0.0000007567080 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013 0.0000005972430 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014 -0.0000001253380 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016 0.0000003886190 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018 -0.0000008999260 No_prior NA NA
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019 -0.0000000386986 No_prior NA NA
## Pr_Like Afterbound
## L_at_Amin_Fem_GP_1 NA OK
## L_at_Amax_Fem_GP_1 NA OK
## VonBert_K_Fem_GP_1 NA OK
## CV_young_Fem_GP_1 NA OK
## CV_old_Fem_GP_1 NA OK
## SR_LN(R0) NA OK
## SR_regime_BLK1repl_1980 NA OK
## InitF_seas_2_flt_2MexCal_S2 NA OK
## Size_inflection_MexCal_S1(1) NA OK
## Size_95%width_MexCal_S1(1) NA OK
## AgeSel_P1_MexCal_S1(1) NA OK
## AgeSel_P2_MexCal_S1(1) NA OK
## AgeSel_P3_MexCal_S1(1) NA OK
## AgeSel_P4_MexCal_S1(1) NA OK
## AgeSel_P5_MexCal_S1(1) NA OK
## AgeSel_P6_MexCal_S1(1) NA OK
## AgeSel_P7_MexCal_S1(1) NA OK
## AgeSel_P8_MexCal_S1(1) NA OK
## AgeSel_P9_MexCal_S1(1) NA OK
## AgeSel_P2_MexCal_S2(2) NA OK
## AgeSel_P3_MexCal_S2(2) NA OK
## AgeSel_P4_MexCal_S2(2) NA OK
## AgeSel_P5_MexCal_S2(2) NA OK
## AgeSel_P6_MexCal_S2(2) NA OK
## AgeSel_P7_MexCal_S2(2) NA OK
## AgeSel_P8_MexCal_S2(2) NA OK
## AgeSel_P9_MexCal_S2(2) NA OK
## Age_inflection_PNW(3) NA OK
## Age_95%width_PNW(3) NA OK
## AgeSel_P2_AT_Survey(4) NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1983 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1985 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1987 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1989 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1991 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1993 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1995 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1997 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_1999 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2001 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2003 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2005 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2007 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2009 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2011 NA OK
## AgeSel_P2_MexCal_S1(1)_BLK3repl_2013 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1983 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1985 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1987 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1989 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1991 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1993 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1995 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1997 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2001 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2003 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2005 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2007 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2009 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2011 NA OK
## AgeSel_P3_MexCal_S1(1)_BLK3repl_2013 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1983 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1985 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1987 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1989 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1991 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1993 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1995 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1997 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_1999 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2001 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2003 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2005 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2007 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2009 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2011 NA OK
## AgeSel_P4_MexCal_S1(1)_BLK3repl_2013 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1983 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1985 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1987 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1989 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1991 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1993 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1995 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1997 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_1999 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2001 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2003 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2005 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2007 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2009 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2011 NA OK
## AgeSel_P5_MexCal_S1(1)_BLK3repl_2013 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1987 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1989 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1991 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1993 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1995 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1997 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_1999 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2001 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2003 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2005 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2007 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2009 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2011 NA OK
## AgeSel_P2_MexCal_S2(2)_BLK7add_2013 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1987 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1989 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1991 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1993 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1995 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1997 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_1999 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2001 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2003 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2005 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2007 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2009 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2011 NA OK
## AgeSel_P3_MexCal_S2(2)_BLK7add_2013 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1987 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1989 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1991 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1993 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1995 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1997 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_1999 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2001 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2003 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2005 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2007 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2009 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2011 NA OK
## AgeSel_P4_MexCal_S2(2)_BLK7add_2013 NA OK
## Age_inflection_PNW(3)_BLK4repl_1999 NA OK
## Age_inflection_PNW(3)_BLK4repl_2001 NA OK
## Age_inflection_PNW(3)_BLK4repl_2003 NA OK
## Age_inflection_PNW(3)_BLK4repl_2005 NA OK
## Age_inflection_PNW(3)_BLK4repl_2007 NA OK
## Age_inflection_PNW(3)_BLK4repl_2009 NA OK
## Age_inflection_PNW(3)_BLK4repl_2011 NA OK
## Age_inflection_PNW(3)_BLK4repl_2013 NA OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2012 NA OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2013 NA OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2014 NA OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2016 NA OK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2018 NA CHECK
## AgeSel_P2_AT_Survey(4)_BLK2repl_2019 NA OK
##
## $maximum_gradient_component
## [1] 0.00238829
##
## $parameters_with_highest_gradients
## Value Gradient
## SR_LN(R0) 16.322700 0.002388290
## SR_regime_BLK1repl_1980 -4.760540 0.000787536
## L_at_Amin_Fem_GP_1 10.132700 0.000412940
## AgeSel_P3_MexCal_S1(1)_BLK3repl_1999 0.862265 0.000372023
## L_at_Amax_Fem_GP_1 23.326300 0.000364136
##
## $Length_Comp_Fit_Summary
## Factor Fleet Recommend_var_adj # N Npos min_Nsamp max_Nsamp mean_Nsamp_in
## 2032 4 1 0.245368 # 30 30 1 89 24.9333
## 2033 4 2 0.419685 # 34 34 3 277 60.1765
## 2034 4 3 0.149375 # 29 17 1 174 80.0588
## 2035 4 4 0.837299 # 9 9 12 31 19.8889
## mean_Nsamp_adj mean_Nsamp_DM DM_theta mean_effN HarMean_effN Curr_Var_Adj
## 2032 24.9333 NA NA 31.2711 6.11783 1
## 2033 60.1765 NA NA 56.9383 25.25510 1
## 2034 80.0588 NA NA 109.6040 11.95880 1
## 2035 19.8889 NA NA 22.7379 16.65300 1
## Fleet_name
## 2032 MexCal_S1
## 2033 MexCal_S2
## 2034 PNW
## 2035 AT_Survey
##
## $Age_Comp_Fit_Summary
## Factor Fleet Recommend_var_adj # Nsamp_adj Npos min_Nsamp max_Nsamp
## 3128 5 1 1 # 30 289 1 28.80
## 3129 5 2 1 # 34 441 1 31.00
## 3130 5 3 1 # 29 163 1 55.60
## 3131 5 4 1 # 9 106 1 9.32
## mean_Nsamp_in mean_Nsamp_adj mean_Nsamp_DM DM_theta mean_effN HarMean_effN
## 3128 2.53052 2.95142 NA NA 31.29410 2.12682
## 3129 3.94177 4.24771 NA NA 35.17100 2.13534
## 3130 6.97374 7.27632 NA NA 37.06180 2.65545
## 3131 1.39585 1.79962 NA NA 7.55662 1.14225
## Curr_Var_Adj Fleet_name
## 3128 1 MexCal_S1
## 3129 1 MexCal_S2
## 3130 1 PNW
## 3131 1 AT_Survey
##
## $SBzero
## [1] 573115
##
## $current_depletion
## [1] 0.1373049
##
## $last_years_SPR
## [1] 0.534885
##
## $SPRratioLabel
## [1] "1-SPR"
##
## $sigma_R_in
## [1] 1
##
## $sigma_R_info
## period N_devs SD_of_devs Var_of_devs mean_SE mean_SEsquared
## 1 Main 36 1.093647 1.196064 0 0
## 2 Early+Main 42 1.080642 1.167786 0 0
## 3 Early+Main+Late 48 1.013388 1.026956 0 0
## sqrt_sum_of_components SD_of_devs_over_sigma_R sqrt_sum_over_sigma_R
## 1 1.093647 1.093647 1.093647
## 2 1.080642 1.080642 1.080642
## 3 1.013388 1.013388 1.013388
## alternative_sigma_R
## 1 1.093647
## 2 1.080642
## 3 1.013388
##
## $rmse_table
## ERA N RMSE RMSE_over_sigmaR mean_BiasAdj
## 1 main 36 1.07835 1.16284 0.900787
## 2 early 6 1.00177 1.00355 0.393099## completed SS_outputSSplotComps(replist = outputSS, kind = "LEN")
SSplotComps(replist = outputSS, kind = "AGE") # nothing happens
# Try using r4ss supporting function
tmp <- SSMethod.TA1.8(fit = outputSS, type = "len",
fleet = 4, fleetnames = outputSS[["FleetNames"]], datonly = FALSE,
printit = FALSE)
# doesn't show compositions by length
unique(outputSS[["lendbase"]]$Yr) # doesn't have data from projection years (2020-2024)## [1] 1982 1983 1985 1987 1988 1989 1990 1992 1993 1994 1995 1996 1997 1998 1999
## [16] 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014
## [31] 1981 1984 1986 1991 2015 2016 2017 2018 2019FleetNames <- outputSS[["FleetNames"]]
# try using ss3sim::get_compfit
# RW: function doesn't exist in the package? but it's in the index...
# get_compfit(report.file = outputSS, name = "len_comp_fit_table")
# run_SSMSE uses expected values for OM catch, so use these in figs
# RW: 'lendbase' only has observed years from historical time series
# termLenComps <- outputSS[["lendbase"]] %>% filter(Fleet == which(FleetNames == "AT_Survey")) %>%
# select(Yr, Seas, Fleet, Bin, Exp)
# Plot terminal age and length comps for OM and EM by iteration
termLenComps <- data.frame()
termAgeComps <- data.frame()
for(i in c(2,4:9)){
outputSS <- SS_output(dir = paste0( "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/",
i, "/cohortGrowthOMandEM_EM_2024"),
dir.mcmc = NULL,
repfile = "Report.sso",
compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
EMLenComps <- outputSS[["batlen"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
pivot_longer(cols = c("6", "6.5", "7", "7.5", "8", "8.5", "9", "9.5", "10", "10.5",
"11", "11.5", "12", "12.5", "13", "13.5", "14", "14.5", "15", "15.5",
"16", "16.5", "17", "17.5", "18", "18.5", "19", "19.5", "20", "20.5",
"21", "21.5", "22", "22.5", "23", "23.5", "24", "24.5", "25", "25.5",
"26", "26.5", "27", "27.5", "28", "28.5", "29", "29.5", "30"),
names_to = "Bin", values_to = "Biomass") %>%
mutate(Bin = as.numeric(Bin),
model_run = "cohortGrowthOMandEM_EM_2024",
iteration = i)
EMAgeComps <- outputSS[["batage"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
pivot_longer(cols = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10"),
names_to = "Age", values_to = "Biomass") %>%
mutate(Age = as.numeric(Age),
model_run = "cohortGrowthOMandEM_EM_2024",
iteration = i)
OMoutputSS <- SS_output(dir = paste0( "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/",
i, "/0_estimate_cohort_growh_OM"),
dir.mcmc = NULL,
repfile = "Report.sso",
compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
OMLenComps <- OMoutputSS[["batlen"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
pivot_longer(cols = c("6", "6.5", "7", "7.5", "8", "8.5", "9", "9.5", "10", "10.5",
"11", "11.5", "12", "12.5", "13", "13.5", "14", "14.5", "15", "15.5",
"16", "16.5", "17", "17.5", "18", "18.5", "19", "19.5", "20", "20.5",
"21", "21.5", "22", "22.5", "23", "23.5", "24", "24.5", "25", "25.5",
"26", "26.5", "27", "27.5", "28", "28.5", "29", "29.5", "30"),
names_to = "Bin", values_to = "Biomass") %>%
mutate(Bin = as.numeric(Bin),
model_run = "0_estimate_cohort_growh_OM",
iteration = i)
OMAgeComps <- OMoutputSS[["batage"]] %>% filter(Yr == 2024, Seas == 2, `Beg/Mid` == "B") %>%
pivot_longer(cols = c("0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "10"),
names_to = "Age", values_to = "Biomass") %>%
mutate(Age = as.numeric(Age),
model_run = "0_estimate_cohort_growh_OM",
iteration = i)
termAgeComps <- rbind(termAgeComps, EMAgeComps, OMAgeComps)
termLenComps <- rbind(termLenComps, EMLenComps, OMLenComps)
}## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = paste0("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/", : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.# RW: no composition data for last year because none provided in 'sample_struct_list' for run_SSMSE()
ggplot(termLenComps, mapping = aes(x = Bin, y = Biomass)) +
geom_col() +
facet_grid(cols = vars(model_run), rows = vars(iteration))
ggplot(termAgeComps, mapping = aes(x = Age, y = Biomass)) +
geom_col() +
facet_grid(cols = vars(model_run), rows = vars(iteration))
Generalized functions applied to Self Test with AT only
Make some generalized functions to apply to different scenarios
bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest",
termYr = 2024, surveyInx = 4)## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 182 rows containing missing values (geom_point).## Warning: Removed 7 row(s) containing missing values (geom_path).
compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest",
termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
# pull recruitment from summary dq
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest", termYr = 2024)## [[1]]
##
## [[2]]## Warning: Removed 14 row(s) containing missing values (geom_path).
#TotCatch_ in ss_summary.sso? or outputSS[["catch"]]
# outputSS <- SS_output(
# dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024",
# dir.mcmc = NULL,
# repfile = "Report.sso",
# compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
#
# catSmry <- outputSS[["catch"]] %>% group_by(Yr) %>%
# # summarize totoal catch within year
# dplyr::summarize(obsCat = sum(Obs),
# expCat = sum(Exp))
catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 14 rows containing missing values (geom_point).## Warning: Removed 7 row(s) containing missing values (geom_path).
FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest", termYr = 2024)
#SmryBio_ in ss_summary.sso? or outputSS[["timeseries"]]
# these aren't equal. SpawnBio matches between these files, but not outputSS[["timeseries"]]$Bio_smry
# outputSS[["timeseries"]] %>% select(Yr, Era, Seas, Bio_smry, `SmryBio_SX:1_GP:1`, SpawnBio)
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthselftest", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthselftest/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
Self-test with acoustic-trawl and age and length comps specified in projection period
bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp",
termYr = 2024, surveyInx = 4)## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 127 rows containing missing values (geom_point).## Warning: Removed 27 row(s) containing missing values (geom_path).
compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp",
termYr = 2024, surveyInx = 4)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp", termYr = 2024)## [[1]]
##
## [[2]]## Warning: Removed 8 row(s) containing missing values (geom_path).
catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 10 rows containing missing values (geom_point).## Warning: Removed 5 row(s) containing missing values (geom_path).
FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp", termYr = 2024)
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM",
scenario = "cohortGrowthself_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/cohortGrowthOMandEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMandEM/cohortGrowthself_compNsamp/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
Test with AT and comp data and fixed parameter EM
bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp",
termYr = 2024, surveyInx = 4)## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 130 rows containing missing values (geom_point).## Warning: Removed 100 row(s) containing missing values (geom_path).
compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp",
termYr = 2024, surveyInx = 4)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp", termYr = 2024)## [[1]]
##
## [[2]]## Warning: Removed 105 row(s) containing missing values (geom_path).
catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 105 rows containing missing values (geom_point).## Warning: Removed 100 row(s) containing missing values (geom_path).
FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp", termYr = 2024)
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "cohortGrowth_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/cohortGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/cohortGrowth_compNsamp/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 95 row(s) containing missing values (geom_path).
# Look at growth and selectivity parameters
# outputSS <- SS_output(dir = file.path("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
# "cohortGrowth_compNsamp", 1, "0_estimate_cohort_growh_OM"),
# dir.mcmc = NULL,
# repfile = "Report.sso",
# compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
# SS_plots(outputSS, plot = c(1, 2, 16, 17, 20, 25, 26))
#
# outputEM <- SS_output(dir = file.path("C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
# "cohortGrowth_compNsamp", 1, "cohortGrowthOMfixedParamsEM_EM_2024"),
# dir.mcmc = NULL,
# repfile = "Report.sso",
# compfile = "CompReport.sso", verbose = FALSE, printstats = FALSE)
# SS_plots(outputEM, plot = c(1, 2, 16, 17, 20, 25, 26))Constant growth OM with AT and comp data and fixed parameter EM
bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp",
termYr = 2024, surveyInx = 4)## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 176 rows containing missing values (geom_point).## Warning: Removed 146 row(s) containing missing values (geom_path).
compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp",
termYr = 2024, surveyInx = 4)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp", termYr = 2024)## [[1]]
##
## [[2]]## Warning: Removed 105 row(s) containing missing values (geom_path).
catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## The supplied data file has 3 sections. Using section = 1.## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of section 1 of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 147 rows containing missing values (geom_point).## Warning: Removed 140 row(s) containing missing values (geom_path).
FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp", termYr = 2024)
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM",
scenario = "constGrowth_compNsamp", termYr = 2024)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/1/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/2/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/3/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/4/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/5/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/6/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowthOMfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/constGrowthOMfixedParamsEM/constGrowth_compNsamp/7/constGrowth_test2_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 133 row(s) containing missing values (geom_path).
Sample size test with cohort growth OM model
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "5pctAnnChangeNsamp10Model", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/10/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp10Model/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 190 row(s) containing missing values (geom_path).
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "5pctAnnChangeNsamp20Model", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/10/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp20Model/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 190 row(s) containing missing values (geom_path).
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "5pctAnnChangeNsamp40Model", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/10/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp40Model/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 190 row(s) containing missing values (geom_path).
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM",
scenario = "5pctAnnChangeNsamp100Model", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/1/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/10/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/2/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/3/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/4/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/5/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/6/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/7/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/8/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/constGrowthfixedParamsEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/cohortGrowthOMfixedParamsEM/5pctAnnChangeNsamp100Model/9/0_estimate_cohort_growh_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]## Warning: Removed 190 row(s) containing missing values (geom_path).
Marginal compositions OM and fixed selectivity EM with high data quality
bDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual",
termYr = 2028, surveyInx = 4)## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 10 rows containing missing values (geom_point).## Warning: Removed 10 row(s) containing missing values (geom_path).
compDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual",
termYr = 2028, surveyInx = 4)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]
recrDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual", termYr = 2028)## [[1]]
##
## [[2]]## Warning: Removed 20 row(s) containing missing values (geom_path).
catchDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, termName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Char version is 3.30
## Numeric version is 3.3## Running SS_readdat_3.30## SS_readdat_3.30 - read version = 3.30## use_meanbodywt (0/1): 0## N_lbinspop:## use_lencomp (0/1): 1## N_lbins: 39## N_agebins: 9## use_MeanSize_at_Age_obs (0/1): 0## N_environ_variables: 0## Read of data file complete. Final value = 999## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.## [[1]]
##
## [[2]]## Warning: Removed 20 rows containing missing values (geom_point).## Warning: Removed 10 row(s) containing missing values (geom_path).
FmsyDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual", termYr = 2028)
age1plusDiagPlots(dir = "C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM",
scenario = "margComps_highDatQual", termYr = 2028)## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/10/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/11/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/12/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/13/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/14/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/15/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/16/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/7/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/8/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_init/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, initName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2020/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2021/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2022/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2023/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2024/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2025/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2026/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2027/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margCompsOMfixedSelexEM_EM_2028/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, grep(y, termNames, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : Some stats skipped because the .cor file not found:C:/Users/rwildermuth/Documents/FutureSeas/SardineMSE/margCompsOMfixedSelexEM/margComps_highDatQual/9/margComp_20210921_OM/ss.cor## Warning in SS_output(dir = file.path(dir, scenario, i, omName), dir.mcmc = NULL, : covar file contains the warning
## 'Variances are 0.0 for first two elements, so do not write '
## input 'covar' changed to FALSE.## [[1]]
##
## [[2]]